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Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3

View ORCID ProfileWen-Feng Zeng, Wei-Qian Cao, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang
doi: https://doi.org/10.1101/2021.02.06.430063
Wen-Feng Zeng
1Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
3University of Chinese Academy of Sciences, Beijing, China
7Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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  • ORCID record for Wen-Feng Zeng
  • For correspondence: wzeng@biochem.mpg.de pyyang@fudan.edu.cn
Wei-Qian Cao
2The Fifth People’s Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
4NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
6The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
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Ming-Qi Liu
2The Fifth People’s Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
4NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
6The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
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Si-Min He
1Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
3University of Chinese Academy of Sciences, Beijing, China
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Peng-Yuan Yang
2The Fifth People’s Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
4NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
5Department of Chemistry, Fudan University, Shanghai, China
6The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
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  • For correspondence: wzeng@biochem.mpg.de pyyang@fudan.edu.cn
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Abstract

We presented a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with monosaccharide-modifications. We developed an algorithm, termed pGlycoSite, to localize the glycosylation sites and estimate the localization probabilities. We designed a number of experiments to validate the accuracy of pGlyco3 as well as other frequently used or recently developed software tools. These experiments showed that pGlyco3 outperformed the other tools on both N- and O-glycopeptide identification accuracy especially at the glycan level, without loss of the sensitivity. pGlyco3 also achieved a superior performance in terms of search speed. As pGlyco3 was shown to be accurate and flexible for glycopeptide search with monosaccharide-modifications, we then discovered a monosaccharide-modification of Hex (or an uncommon monosaccharide) “Hex+17.027 Da” on both O-mannose and N-glycopeptides in yeast samples, and confirmed this monosaccharide based on released N-glycans and isotopic labelling data. pGlyco3 is freely available on https://github.com/pFindStudio/pGlyco3/releases.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 08, 2021.
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Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3
Wen-Feng Zeng, Wei-Qian Cao, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang
bioRxiv 2021.02.06.430063; doi: https://doi.org/10.1101/2021.02.06.430063
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Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3
Wen-Feng Zeng, Wei-Qian Cao, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang
bioRxiv 2021.02.06.430063; doi: https://doi.org/10.1101/2021.02.06.430063

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